Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Pbrm1

Cell type

Cell type Class
Others
Cell type
OP9
Tissue
Bone Marrow/Stroma
Cell Type
Embryonic Stem Cells, Macrophage

Attributes by original data submitter

Sample

source_name
shCtrl
cell line
OP9
cell type
Stromal Cell line
chip antibody
PBRM1 (Bethyl Laboratories, Cat. A301-591A , Lot A301-591A-2)
knockdown
shCtrl

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with specific antibody. ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer's instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 277 ± 13bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
54135516
Reads aligned (%)
96.3
Duplicates removed (%)
83.1
Number of peaks
185 (qval < 1E-05)

mm9

Number of total reads
54135516
Reads aligned (%)
96.2
Duplicates removed (%)
83.2
Number of peaks
156 (qval < 1E-05)

Base call quality data from DBCLS SRA